SBC logo Authors: Amine Heddad, Andrea Krings, Markus Brameier and Bob MacCallum, Stockholm Bioinformatics Center, Stockholm University, Sweden.

NucPred

Fetching P07751 from www.uniprot.org...

The NucPred score for your sequence is 0.91 (see score help below)

   1  MDPSGVKVLETAEDIQERRQQVLDRYHRFKELSSLRRQKLEDSYRFQFFQ    50
  51  RDADELGKWIQEKLQIASDENYKDPSNLQGKLQKHQAFEAEVQANSGAIV   100
 101  KLDETGNQMINEGHFASETIRTRLQELHRLWELLLEKMREKGVKLLQAQK   150
 151  LVQFLRECEDVMDWINDKEAIVTSEELGQDLEHVEVLQKKFEEFQTDLAA   200
 201  HEERVNEVNQFAGKLIQEQHPEEELIKSKQDEVNASWQRLKGLAQQRQGK   250
 251  LFGAAEVQRFNRDVDETISWIKEKGQLMASDDFGRDLASVQALLRKHEGL   300
 301  ERDLAAFHHKVKALCAEADRLQQSHPINASQIQVKREELIANWEQIRTLA   350
 351  AERHARLNDSYRLQRFLADFRDLTSWVTEMKALINADELANDVAGAEALL   400
 401  DRHQEHKGEIDAHEDSFRSADESGQALLAAGHYASDEVKEKLTILSDERS   450
 451  ALLELWELRRQQYEQCMDLQLFYRDTEQVDNWMSKQEAFLLNEDLGDSLD   500
 501  SVEALLKKHEDFEKSLSAQEEKITALDEFATKLIQNNHYAMDDVATRRDA   550
 551  LLSRRNALHERAMKRRAQLADSFHLQQFFRDSDELKSWVNEKMKTATDEA   600
 601  YKDPSNLQGKVQKHQAFEAELSANQSRIDALEKAGQKLIDVNHYASDEVA   650
 651  ARMNEVISLWKKLLEATELKGIKLREANQQQQFNRNVEDIELWLYEVEGH   700
 701  LASDDYGKDLTSVQNLQKKHALLEADVAAHQDPIDGITIQARQFQDAGHF   750
 751  DADNIKKKQEALVARYEALKDPMVARKQKLADSLRLQQLFRDIEDEETWI   800
 801  REKEPIAASTNRGKDLIGVQNLLKKHQALQAEIAGHEPRIKAVTQKGNAM   850
 851  VEEGHFAAEDVKIKLNELNQKWDSLKAKASQRRQDLEDSLQAQQYFADAN   900
 901  EAQSWMREKEPIVGSTDYGKDEDSAEALLKKHEALMSDLSAYGSSIQALR   950
 951  EQAQSCRQQVAPTDDETGKELVLALYDYQEKSPREVTMKKGDILTLLNST  1000
1001  NKDWWKVEVNDRQGFVPAAYVKKLDPAQSASRENLLEEQGSIALRQEQID  1050
1051  NQTLITKEVGSVSLRMKQVEELYHSLLELGEKRKGMLEKSCKKFMLFREA  1100
1101  NELQQWINEKEAALTNEEVGADLEQVEVLQKKFDDFQKDLKANESRLKDI  1150
1151  NKVANDLESEGLMAEEVQAVEHQEVYGMMPRDETDSKTVSPWKSARMMVH  1200
1201  TVATFNSIKELNERWRSLQQLAEERSQLLGSADEVQRFHRDADETKEWIE  1250
1251  EKNQALNTDNYGHDLASVQALQRNDEGFERDLAALGDKVNSLGETAQRLI  1300
1301  QSHPELAEDLQEKCTELNQAWSSLGKRADQRKEKLGDSHDLQRFLSDFRD  1350
1351  LMSWINGIRGLVSSDELAKDVTGAEALLERHQEHRTEIDARAGTFQAFEQ  1400
1401  FGQQLLARGHYASPEIKEKLDILDQERTDLEKAWVQRRMMLDQCLELQLF  1450
1451  HRDCEQAENWMAAREAFLNTEDKGDSLDSVEALIKKHEDFDKAINVQEEK  1500
1501  IAVLQSFADQLIAADHYAKGVIANRRNEVLDRWRRLKAQMIEKRSKLGES  1550
1551  QTLQQFSRDVDEIEAWISEKLQTASDESYKDPTNIQLSKLLSKHQKHQAF  1600
1601  EAELHANADRIRGVIEMGNPLIERGACAGSEDAVKARLAALADQWEFLVQ  1650
1651  KSSEKSQKLKEANKQQNFNTGIKDFDFWLSEVEALLASEDYGKDLASVNN  1700
1701  LLKKHQLLEADISAHEDRLKDLNSQADSLMTSSAFDTSQVKDKRETINGR  1750
1751  FQRIKSMAAARRAKLNESHRLHQFFRDMDDEESWIKEKKLLVSSEDYGRD  1800
1801  LTGVQNLRKKHKRLEAELAAHEPAIQGVLDTGKKLSDDNTIGKEEIQQRL  1850
1851  AQFVDHWKELKQLAAARGQRLEESLEYQQFVANVEEEEAWINEKMTLVAS  1900
1901  EDYGDTLAAIQGLLKKHEAFETDFTVHKDRVNDVCANGEDLIKKNNHHVE  1950
1951  NITAKMKGLKGKVSDLEKAAAQRKAKLDENSAFLQFNWKADVVESWIGEK  2000
2001  ENSLKTDDYGRDLSSVQTLLTKQETFDAGLQAFQQEGIANITALKDQLLA  2050
2051  AKHIQSKAIEVRHASLMKRWNQLLANSAARKKKLLEAQEHFRKVEDLFLT  2100
2101  FAKKASAFNSWFENAEEDLTDPVRCNSLEEIKALREAHDAFRSSLSSAQA  2150
2151  DFNQLAELDRQIKSFRVASNPYTWFTMEALEETWRNLQKIIKERELELQK  2200
2201  EQRRQEENDKLRQEFAQHANAFHQWIQETRTYLLDGSCMVEESGTLESQL  2250
2251  EATKRKHQEIRAMRSQLKKIEDLGAAMEEALILDNKYTEHSTVGLAQQWD  2300
2301  QLDQLGMRMQHNLEQQIQARNTTGVTEEALKEFSMMFKHFDKDKSGRLNH  2350
2351  QEFKSCLRSLGYDLPMVEEGEPDPEFESILDTVDPNRDGHVSLQEYMAFM  2400
2401  ISRETENVKSSEEIESAFRALSSERKPYVTKEELYQNLTREQADYCISHM  2450
2451  KPYMDGKGRELPSAYDYIEFTRSLFVN                         2477

Positively and negatively influencing subsequences are coloured according to the following scale:

(non-nuclear) negative ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| positive (nuclear)

with NucPred



If you find NucPred useful, please cite this paper:
NucPred - Predicting Nuclear Localization of Proteins. Brameier M, Krings A, Maccallum RM. Bioinformatics, 2007. PubMed id: 17332022
The authors also look forward to your comments and suggestions.

What does the NucPred score mean?

You have to decide on a NucPred score threshold. Sequences which score greater than or equal to this threshold are predicted to spend some time in the nucleus. Higher thresholds yield fewer predicted nuclear proteins, but these predictions are more accurate (you can have higher confidence in them). The table below gives more details of the performance of NucPred estimated using the sequences it was trained on (by cross-validation). Another benchmark is available in the Bioinformatics 2007 paper.

NucPred score threshold Specificity Sensitivity
see above fraction of proteins predicted to be nuclear that actually are nuclear fraction of true nuclear proteins that are predicted (coverage)
0.10 0.45 0.88
0.20 0.52 0.83
0.30 0.57 0.77
0.40 0.63 0.69
0.50 0.70 0.62
0.60 0.71 0.53
0.70 0.81 0.44
0.80 0.84 0.32
0.90 0.88 0.21
1.00 1.00 0.02

Sequences which score >= 0.8 with NucPred and which are predicted by PredictNLS to contain an NLS have been shown to be 93% correct with a coverage of 16%. (PredictNLS by itself is 87% correct with 26% coverage on the same data.)

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